[BioC] Help with the weaver example from limma package

Gordon K Smyth smyth at wehi.EDU.AU
Thu Jun 23 09:09:26 CEST 2011

Hi Marcus,

The file you want is called "genelist.txt".  You can use this in place of 
"091701RikenUpdatev3.txt".  This is a simplified version of the complete 
probe annotation file "091701RikenUpdatev3.txt", in which the gene 
identifiers are removed, because I didn't have permission to make the 
complete data publicly available.  The "spottypes.txt" is also slighltly 
different from that used in the limma User's Guide.  Sorry for the 

Best wishes

> Date: Mon, 20 Jun 2011 19:50:01 -0400
> From: Marcus Nunes <marcus.nunes at gmail.com>
> To: Bioconductor <bioconductor at r-project.org>
> Subject: [BioC] Help with the weaver example from limma package
> Content-Type: text/plain
> Hello all
> I'm trying to figure out how to mimic the example given in Weaver Mutant
> Data: A 2x2 Factorial Experiment with Two-Color Data (page 81 of this
> manual:
> http://bioconductor.org/packages/2.6/bioc/vignettes/limma/inst/doc/usersguide.pdf)
> There is a line of code, in page 82, that says
>> Annotation <- read.delim("091701RikenUpdatev3.txt", header = TRUE,
> comment.char="",
> + quote="\"", as.is = TRUE, check.names=FALSE
> I downloaded the dataset available at
> http://bioinf.wehi.edu.au/limma/data/weaver.zip and I can't find this
> file 091701RikenUpdatev3.txt. I already searched the internet and I couldn't
> figure out what I have to do. I'll be very glad if you know how to help me.
> Thanks
> -- 
> Marcus Nunes

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